Cyber Zeed - the villains who previously tried to destroy the world - are back. Zeed's army is stealing plutonium from power plants around the world. Their goal is to melt this planet down. All the world's nations have joined forces in an attempt to put an end to this chaos. Thousands of troops have been sent out, but none of them returned.
A lone ninja has appeared - the grandson of the brave ninja who defeated Neo Zeed years ago. He is Joe Musashi, the most skilled martial artist in the world and wielder of the four types of Ninjutsu - fire, tornado, lightning and earth. He is the only hope. Cyber Zeed must be destroyed once and for all.
The player controls Shinobi and finishes each level by running from left to right while defeating enemies and picking up power-ups. Action is limited to jumping, crouching and attacking. Attacking is done with a short range katana slash. However throughout the game shuriken as well as machine guns can be found in limited supply. Each stage requires Shinobi to defeat every enemy on screen, otherwise he cannot move further.
In total there are six rounds to complete, each one consisting of 2 to 3 different scenes. The final scene of a round is a battle against a powerful boss character.